Biochemistry in healthy and neoplastic human tissues: metabolic alteration revealed by HR-MAS nuclear magnetic resonance spectroscopy

This thesis is focused on the metabolomic study of human cancer tissues by ex vivo High Resolution-Magic Angle Spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. This new technique allows for the acquisition of spectra directly on intact tissues (biopsy or surgery), and it has become very important for integrated metabonomics studies. The objective is to identify metabolites that can be used as markers for the discrimination of the different types of cancer, for the grading, and for the assessment of the evolution of the tumour. Furthermore, an attempt to recognize metabolites, that although involved in the metabolism of tumoral tissues in low concentration, can be important modulators of neoplastic proliferation, was performed. In addition, NMR data was integrated with statistical techniques in order to obtain semi-quantitative information about the metabolite markers. In the case of gliomas, the NMR study was correlated with gene expression of neoplastic tissues. Chapter 1 begins with a general description of a new “omics” study, the metabolomics. The study of metabolism can contribute significantly to biomedical research and, ultimately, to clinical medical practice. This rapidly developing discipline involves the study of the metabolome: the total repertoire of small molecules present in cells, tissues, organs, and biological fluids. Metabolomic approaches are becoming increasingly popular in disease diagnosis and will play an important role on improving our understanding of cancer mechanism. Chapter 2 addresses in more detail the basis of NMR Spectroscopy, presenting the new HR-MAS NMR tool, that is gaining importance in the examination of tumour tissues, and in the assessment of tumour grade. Some advanced chemometric methods were used in an attempt to enhance the interpretation and quantitative information of the HR-MAS NMR data are and presented in chapter 3. Chemometric methods seem to have a high potential in the study of human diseases, as it permits the extraction of new and relevant information from spectroscopic data, allowing a better interpretation of the results. Chapter 4 reports results obtained from HR-MAS NMR analyses performed on different brain tumours: medulloblastoma, meningioms and gliomas. The medulloblastoma study is a case report of primitive neuroectodermal tumor (PNET) localised in the cerebellar region by Magnetic Resonance Imaging (MRI) in a 3-year-old child. In vivo single voxel 1H MRS shows high specificity in detecting the main metabolic alterations in the primitive cerebellar lesion; which consist of very high amounts of the choline-containing compounds and of very low levels of creatine derivatives and N-acetylaspartate. Ex vivo HR-MAS NMR, performed at 9.4 Tesla on the neoplastic specimen collected during surgery, allows the unambiguous identification of several metabolites giving a more in-depth evaluation of the metabolic pattern of the lesion. The ex vivo HR-MAS NMR spectra show higher detail than that obtained in vivo. In addition, the spectroscopic data appear to correlate with some morphological features of the medulloblastoma. The present study shows that ex vivo HR-MAS 1H NMR is able to strongly improve the clinical possibility of in vivo MRS and can be used in conjunction with in vivo spectroscopy for clinical purposes. Three histological subtypes of meningiomas (meningothelial, fibrous and oncocytic) were analysed both by in vivo and ex vivo MRS experiments. The ex vivo HR-MAS investigations are very helpful for the assignment of the in vivo resonances of human meningiomas and for the validation of the quantification procedure of in vivo MR spectra. By using one- and two dimensional experiments, several metabolites in different histological subtypes of meningiomas, were identified. The spectroscopic data confirmed the presence of the typical metabolites of these benign neoplasms and, at the same time, that meningomas with different morphological characteristics have different metabolic profiles, particularly regarding macromolecules and lipids. The profile of total choline metabolites (tCho) and the expression of the Kennedy pathway genes in biopsies of human gliomas were also investigated using HR-MAS NMR, and microfluidic genomic cards. 1H HR-MAS spectra, allowed the resolution and relative quantification by LCModel of the resonances from choline (Cho), phosphorylcholine (PC) and glycerolphorylcholine (GPC), the three main components of the combined tCho peak observed in gliomas by in vivo 1H MRS spectroscopy. All glioma biopsies depicted an increase in tCho as calculated from the addition of Cho, PC and GPC HR-MAS resonances. However, the increase was constantly derived from augmented GPC in low grade NMR gliomas or increased PC content in the high grade gliomas, respectively. This circumstance allowed the unambiguous discrimination of high and low grade gliomas by 1H HR-MAS, which could not be achieved by calculating the tCho/Cr ratio commonly used by in vivo 1H MR spectroscopy. The expression of the genes involved in choline metabolism was investigated in the same biopsies. The present findings offer a convenient procedure to classify accurately glioma grade using 1H HR-MAS, providing in addition the genetic background for the alterations of choline metabolism observed in high and low gliomas grade. Chapter 5 reports the study on human gastrointestinal tract (stomach and colon) neoplasms. The human healthy gastric mucosa, and the characteristics of the biochemical profile of human gastric adenocarcinoma in comparison with that of healthy gastric mucosa were analyzed using ex vivo HR-MAS NMR. Healthy human mucosa is mainly characterized by the presence of small metabolites (more than 50 identified) and macromolecules. The adenocarcinoma spectra were dominated by the presence of signals due to triglycerides, that are usually very low in healthy gastric mucosa. The use of spin-echo experiments enable us to detect some metabolites in the unhealthy tissues and to determine their variation with respect to the healthy ones. Then, the ex vivo HR-MAS NMR analysis was applied to human gastric tissue, to obtain information on the molecular steps involved in the gastric carcinogenesis. A microscopic investigation was also carried out in order to identify and locate the lipids in the cellular and extra-cellular environments. Correlation of the morphological changes detected by transmission (TEM) and scanning (SEM) electron microscopy, with the metabolic profile of gastric mucosa in healthy, gastric atrophy autoimmune diseases (AAG), Helicobacter pylori-related gastritis and adenocarcinoma subjects, were obtained. These ultrastructural studies of AAG and gastric adenocarcinoma revealed lipid intra- and extra-cellularly accumulation associated with a severe prenecrotic hypoxia and mitochondrial degeneration. A deep insight into the metabolic profile of human healthy and neoplastic colon tissues was gained using ex vivo HR-MAS NMR spectroscopy in combination with multivariate methods: Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA). The NMR spectra of healthy tissues highlight different metabolic profiles with respect to those of neoplastic and microscopically normal colon specimens (these last obtained at least 15 cm far from the adenocarcinoma). Furthermore, metabolic variations are detected not only for neoplastic tissues with different histological diagnosis, but also for those classified identical by histological analysis. These findings suggest that the same subclass of colon carcinoma is characterized, at a certain degree, by metabolic heterogeneity. The statistical multivariate approach applied to the NMR data is crucial in order to find metabolic markers of the neoplastic state of colon tissues, and to correctly classify the samples. Significant different levels of choline containing compounds, taurine and myoinositol, were observed. Chapter 6 deals with the metabolic profile of normal and tumoral renal human tissues obtained by ex vivo HR-MAS NMR. The spectra of human normal cortex and medulla show the presence of differently distributed osmolytes as markers of physiological renal condition. The marked decrease or disappearance of these metabolites and the high lipid content (triglycerides and cholesteryl esters) is typical of clear cell renal carcinoma (RCC), while papillary RCC is characterized by the absence of lipids and very high amounts of taurine. This research is a contribution to the biochemical classification of renal neoplastic pathologies, especially for RCCs, which can be evaluated by in vivo MRS for clinical purposes. Moreover, these data help to gain a better knowledge of the molecular processes envolved in the onset of renal carcinogenesis.

Outcome analysis of predictors in locally advanced pancreatic cancer

Guidelines report a wide range of options in locally advanced pancreatic cancer (LAPC): definitive chemotherapy or chemoradiotherapy or the emerging stereotactic body radiotherapy (SBRT) (+/- chemotherapy). On behalf of the AIRO (Italian Association of Radiation Oncology and Clinical Oncology) Gastrointestinal Study Group, we collected retrospective clinical data on 419 LAPC from 15 Italian centers. The study protocol (PAULA-1: Pooled Analysis in Unresectable Locally Advanced pancreatic cancer) was approved by institutional review board of S. Orsola-Malpighi Hospital (201/2015/O/OssN). From this large database we performed tree different studies. The first was a retrospective study about 56 LAPC treated with SBRT at a median biologically equivalent dose of 48 Gy +/- chemotherapy. We demonstrated a statistically significant impact of biologically equivalent dose based on an α/β ratio of 10Gy ≥ 48Gy for local control (LC) (p: 0.045) and overall survival (p: 0.042) in LAPC. The second was a retrospective matched-cohort case-control study comparing SBRT (40 patients) and chemoradiation (40 patients) in LAPC in terms of different endpoints. Our findings suggested an equivalence in terms of most outcomes among the two treatments and an advantage of SBRT in terms of LC (p: 0.017). The third study was a retrospective comparison of definitive chemotherapy, chemoradiotherapy and SBRT (+/- chemotherapy) in terms of different outcomes in LAPC. A predictive model for LC in LAPC was also developed reaching an AUC of 68% (CI 58,7%-77,4%). SBRT treatment emerged as a positive predictive factor for improved LC. Findings deriving from our three studies suggest that SBRT is comparable to standard of care (definitive chemotherapy and chemoradiotherapy) in terms of outcomes. SBRT seems to be an emerging therapeutic option in LAPC significantly improving local control. Furthermore, we have shown the potential of a predictive model for LC. Randomized trials are needed to compare these different therapeutic options in LAPC.

Analysis of extracellular vesicles from patients with advanced pancreatic cancer identifies miRNAs with predictive value for treatment with gemcitabine + nab-paclitaxel

Pancreatic cancer (PC) is the seventh leading cause of cancer death. Despite recent therapy advancements, 5-year survival is 11%. Resistance to therapy is common, and no predictive factors, except for BRCA1/2 and PALB2 mutations, can drive treatment selection. Based on the easy isolation of extracellular vesicles (EVs) from blood and the role of EV-borne miRNAs in chemoresistance, we analyzed EVs and their miRNA content in order to identify predictive factors. First, we analyzed samples from 28 PC patients and 7 healthy subjects, in order to establish methods for isolation and analysis of EVs and their miRNA content. We observed a significantly different expression of 28 miRNAs, including oncogenic or tumor suppressor miRNAs, showing the ability of our approach to detect candidate biomarkers. Then, we analyzed samples of 21 advanced PC patients, collected before first-line treatment with gemcitabine + nab-paclitaxel, and compared findings in responders and non-responders. EVs have been analyzed with Nanoparticle tracking analysis, flow cytometry and RNA-Seq; then, laboratory results have been matched with clinical data. Nanoparticle tracking analysis did not show any significant difference. Flow cytometry showed a lower expression of SSE4 and CD81 in responders. Finally, miRNA analysis showed 25 upregulated and 19 downregulated miRNAs in responders. In particular, in responders we observed upregulation of miR-141-3p, miR-141-5p, miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-375-3p, miR-429, miR-545-5p. These miRNAs have targets with a previously reported role in PC. In conclusion, we show the feasibility of the proposed approach to identify EV-derived biomarkers with predictive value for therapy with gemcitabine + nab-paclitaxel in PC. Our findings highlight the possibility to exploit liquid biopsy for personalized treatment in PC, in order to maximize chances of response and patients’ outcome. These findings are worthy of further investigation: in the same setting, with different chemotherapy schedules, and in different disease settings such as preoperative therapy.

Studio pancreatic cystic follow-up, an international collaboration (PACYFIC study). Valutazione prospettica della sorveglianza delle cisti pancreatiche basato sulla consensus Europea sui tumori cistici del pancreas.

Introduzione Nel 2014 è stato proposto un protocollo di studio riguardante la sorveglianza delle lesioni cistiche del pancreas (intese come IPMN) e denominato PACYFIC Study. Obiettivi Obiettivo primario era di stabilire l’impatto di un programma di sorveglianza in termini di pazienti arruolati e pazienti con indicazione chirurgica. Obiettivi secondari erano: 1) stabilire l’impatto dei fattori demografici, clinici, radiologici e della strategia di sorveglianza sull’indicazione chirurgica, sulla capacità individuare le lesioni maligne, sulla sopravvivenza. Materiali e Metodi Lo studio su cui si è basata la raccolta dei dati è uno studio di tipo prospettico, di coorte, multicentrico, internazionale. Lo studio ha incluso gli individui con una IPMN, di nuova o pregressa diagnosi, che giustifichi una sorveglianza o il trattamento chirurgico. I dati clinici, demografici, radiologici e chirurgici sono stati raccolti in un database prospettico. Le variabili discrete sono state espresse come frequenza e percentuale. Le continue come medie e deviazioni standard o mediane e range interquartile (IQR). Per l’analisi statistica sono stati utilizzati il test di Fischer, il test del Chi quadro, il test di Spearman, il test di Student. L’analisi multivariata è stata eseguita utilizzando la regressione logistica espressa come Odds Ratio e intervallo di confidenza al 95 %. Per la sopravvivenza è stato utilizzato il metodo di Kaplan-Meier. L’analisi multivariata sulle sopravvivenze è stata eseguita mediante la regressione di Cox. Risultati Il protocollo di sorveglianza ha permesso l'arruolamento di 516 pazienti. 53 pazienti hanno raggiunto l'indicazione chirurgica. La sopravvivenza globale della coorte è stata di 326.8± 9.1 mesi. I fattori predittivi la sopravvivenza sono risultati età (OR 1.07, P-value<0.001), sesso (OR 1.82, P-value=0.006), ittero, noduli murali (OR 4.84, P-value=0.018 e OR 2.19, P-value=0.016), chirurgia (OR 0.46, P-value 0.038). Conclusioni L'introduzione del protocollo di sorveglianza ha portato ad un aumento di identificazione di lesioni e ha avuto impatto sulla sopravvivenza